Polygenic Score (PGS) ID: PGS000679

Predicted Trait
Reported Trait Creatinine in urine [umol/L]
Mapped Trait(s) creatinine clearance measurement (EFO_0007934)
Released in PGS Catalog: Feb. 3, 2021
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Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Creatinine_in_urine
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 5,469
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001407 PSS000669|
African Ancestry|
5,789 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine in urine [umol/L] — — R²: 0.11165
Spearman's ρ: 0.035		 Age, sex, PCs(1-40) —
PPM001442 PSS000670|
East Asian Ancestry|
1,045 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine in urine [umol/L] — — R²: 0.16547
Spearman's ρ: 0.049		 Age, sex, PCs(1-40) —
PPM001477 PSS000671|
European Ancestry|
22,875 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine in urine [umol/L] — — R²: 0.16134
Spearman's ρ: 0.068		 Age, sex, PCs(1-40) —
PPM001547 PSS000673|
European Ancestry|
62,142 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine in urine [umol/L] — — R²: 0.14919
Spearman's ρ: 0.077		 Age, sex, PCs(1-40) —
PPM001512 PSS000672|
South Asian Ancestry|
7,009 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Creatinine in urine [umol/L] — — R²: 0.16585
Spearman's ρ: 0.056		 Age, sex, PCs(1-40) —
PPM007320 PSS007051|
African Ancestry|
6,241 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine (enzymatic) in urine — — R²: 0.09395 [0.08045, 0.10745]
Incremental R2 (full-covars): 0.0
PGS R2 (no covariates): 0.00117 [-0.00049, 0.00283]		 age, sex, UKB array type, Genotype PCs —
PPM007321 PSS007052|
East Asian Ancestry|
1,644 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine (enzymatic) in urine — — R²: 0.13143 [0.10159, 0.16127]
Incremental R2 (full-covars): 0.0
PGS R2 (no covariates): 0.00022 [-0.00117, 0.0016]		 age, sex, UKB array type, Genotype PCs —
PPM007322 PSS007053|
European Ancestry|
24,146 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine (enzymatic) in urine — — R²: 0.12535 [0.11766, 0.13304]
Incremental R2 (full-covars): 0.0
PGS R2 (no covariates): 0.00508 [0.00332, 0.00685]		 age, sex, UKB array type, Genotype PCs —
PPM007323 PSS007054|
South Asian Ancestry|
7,474 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine (enzymatic) in urine — — R²: 0.11942 [0.10595, 0.1329]
Incremental R2 (full-covars): 0.0
PGS R2 (no covariates): 0.00174 [-0.0001, 0.00358]		 age, sex, UKB array type, Genotype PCs —
PPM007324 PSS007055|
European Ancestry|
65,669 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Creatinine (enzymatic) in urine — — R²: 0.10867 [0.10423, 0.1131]
Incremental R2 (full-covars): 0.0
PGS R2 (no covariates): 0.00504 [0.00398, 0.00611]		 age, sex, UKB array type, Genotype PCs —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS007051 — — 6,241 individuals — African unspecified — UKB —
PSS007052 — — 1,644 individuals — East Asian — UKB —
PSS007053 — — 24,146 individuals — European non-white British ancestry UKB —
PSS007054 — — 7,474 individuals — South Asian — UKB —
PSS007055 — — 65,669 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000669 — — 5,789 individuals — African unspecified — UKB —
PSS000670 — — 1,045 individuals — East Asian — UKB —
PSS000671 — — 22,875 individuals — European Non-British White UKB —
PSS000672 — — 7,009 individuals — South Asian — UKB —
PSS000673 — — 62,142 individuals — European
(British)		 — UKB —